In recent years, the clinical laboratory community has vigorously debated the merit of microbiology tests versus their newer molecular counterparts for infectious disease cases. But today, several trends in the field are increasingly shifting labs toward molecular diagnostics and away from the highly laborious microbiology tests, even those long considered to be the gold standard for a specific pathogen. Microbiology will always play a key role in the clinical lab, but molecular diagnostics has been making a cogent case that it will be a staple of laboratory science as well, and in some cases will supplant the older technologies.
Demand for molecular alternatives is being driven in large part by the need for faster results. As molecular tests have improved, their turnaround time has been significantly reduced—but microbiology tests by their nature simply cannot be run any more quickly. It is now possible to generate clinically actionable results from molecular diagnostics in as little as one to a few hours. Related to the interest in shorter turnaround, the antibiotic resistance crisis has made it essential to identify potential resistance markers as soon as possible to avoid prolonged exposure to empiric broad spectrum antibiotics for infectious disease patients. Microbiology methods typically require several days to generate this kind of information, but antimicrobial stewardship programs striving to get patients on targeted treatments cannot afford this kind of delay. Molecular tests now allow clinical lab teams to deliver this data within the first day.
The skill sets of laboratorians is another relevant factor in the ongoing shift. Modern training focuses on molecular testing, and clinical laboratory scientists who have the skills required to perform microbiology testing are becoming scarce. At the same time, the complexity of molecular testing has been greatly reduced since these tests were first introduced. Modern sample-to-answer platforms have push-button functionality and can be operated with minimal expertise—allowing the microbiology lab to still perform the testing, but in a molecular format.
Finally, the clinical lab understanding of molecular test results has evolved in recent years. It was once thought that molecular tests, with their higher sensitivity, yielded too many false positives when compared to results from culture-based tests. However, it is now acknowledged that the positive results were correct; it was the microbiology tests that were less sensitive and thus generating false negative results.1,2 The great accuracy of molecular tests is now broadly accepted in the laboratory community.
Microbiology: strengths and limitations
Even the best microbiology tests are compromised to a degree by subjectivity. Consider the conventional workflow for a new specimen arriving at the microbiology lab. Samples are distributed across benches, typically based on the type of infection, for initial plating, Gram stain, culture, and additional biochemical analysis. That may sound very precise, but the reality is that there are many judgment calls woven throughout the process. Selecting the part of the specimen to plate is also imprecise; laboratorians have to hope that the microscopic amount used harbors the pathogen, because there is no way to know for sure.
Plating involves growing the specimen on different types of media, based on the typical pathogens expected. Once the organism has been grown in culture, the microbiologist must decide which colonies are significant enough to merit follow-on analysis. Choosing these colonies has major implications for the quality of the results generated and may allow clinically relevant information to be missed. If antibiotic susceptibility testing has to be done, that involves choosing another pure, isolated colony—or what the laboratorian hopes is a pure colony—followed by inoculation and more culturing, this time in the presence of antibiotics. Lab staff running these tests have to measure the zone of inhibition, which is not an exact science. Organisms can also be partly resistant, which can make it even more challenging to confidently identify the resistance pattern.
This is not to say that microbiology tests are unreliable. For decades, these tests have been invaluable in clinical laboratories. However, it is important to understand their strengths and weaknesses when evaluating alternatives. The subjectivity is a real drawback to microbiology tests and should be recognized as such when more accurate molecular tests become available for the same application.
Another limitation of microbiology tests is their turnaround time. Culture-based tests require time to grow the organism, which may happen overnight or may take significantly longer. Standard testing protocols involve maintaining negative cultures for several days to be sure nothing starts growing; in the case of tuberculosis, labs have to keep cultures as long as six to eight weeks, while molecular results can be generated in just a few hours.
The impact of antibiotic resistance
Perhaps the strongest driver for the shift to rapid molecular diagnostics stems from the antibiotic resistance crisis. Treating patients with broad-spectrum antibiotics is no longer the optimal approach because it is more likely to trigger resistance. Ideally, pathogen identification and analysis of resistance markers should happen fast enough to get the patient on a targeted antibiotic to control the infection without compounding the resistance problem. Microbiology tests cannot meet this time pressure, but molecular tests can.
It’s worth a quick review of the state of antibiotic resistance to recognize how high the stakes are for getting patients off of broad-spectrum antibiotics. From infectious diseases that were once well controlled with conventional antibiotics to quickly evolving strains found to be resistant to all known classes of drugs, the public health threat is alarming. According to research from the Wellcome Trust and UK government, some 700,000 people die each year globally from infections that are drug-resistant.3 If the pace continues, this number is predicted to grow to 10 million by the year 2050.
The World Health Organization (WHO), which is closely monitoring trends in antibiotic resistance, has reported that cases of carbapenem-resistant Klebsiella pneumoniae, a pathogen that defies even the last-resort treatment, have been found all over the world.4,5 For E. coli infections, there are now areas where more than half of patients cannot be treated with fluoroquinolones, a type of antibiotic that came out in the 1980s.
According to the WHO and the U.S. Centers for Disease Control and Prevention (CDC), some of the most dangerous drug-resistant pathogens include Clostridium difficile, carbapenem-resistant Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA), tuberculosis, and Neisseria gonorrhoeae.6,7 Remarkably, MRSA contributes to more deaths in the United States each year than homicide, Parkinson’s disease, emphysema, and HIV/AIDS together.8
Meanwhile, multidrug resistance is becoming increasingly common, making treatment selection that much more challenging. In 2011, the Infectious Diseases Society of America found that 63 percent of infectious disease experts who responded to a survey reported treating at least one patient whose infection was resistant to all available antibiotics in the prior year.9
In addition to antibiotic resistance, the increasing recognition of the dangers of co-infections has also put more focus on molecular testing for infectious disease. Unlike microbiology tests, which typically lead to a single result, panel-based molecular diagnostics that test for a number of different organisms or closely related strains can identify cases where patients have more than one infection. During the Zika outbreak in the Americas, for instance, understanding whether a patient with Zika was co-infected with endemic pathogens such as dengue virus proved important for treatment and prognosis.
As demand for rapid molecular testing rises, technology trends have made these platforms stronger alternatives to microbiology tests. Initially, molecular tests were frequently classified as high-complexity, limiting the number of clinical labs or laboratorians qualified to use them. As the technology behind these tests has evolved, however, their ease of use has improved substantially. It is common today to find “sample-to-answer” molecular diagnostics platforms for which operation is as simple as loading samples into a cassette, inserting the cassette in an instrument, and pushing a button to start the reaction. Since these systems require minimal hands-on time or technical expertise, they are now suitable options for almost any clinical lab and can even make it easier to design new laboratory-developed tests. Molecular tests also eliminate much of the guesswork involved in microbiology workflows. Because they amplify what is in the sample, there is far less chance to miss the causal pathogen.
The first molecular tests were typically designed to detect just one organism. Now, panel-based tests are readily available for infections ranging from gastrointestinal to respiratory and more. The advantage to this approach is speed: in the time it takes to run a single test, clinical labs can generate results about many candidates that could be causing the infection. If all of these results had to be run through standard microbiology, staff could be busy for days before any medically relevant information could be conveyed to the treating physician. The first multiplex panels that were widely adopted in clinical labs were for respiratory viruses. Not only was the multiplexing an advance, but many of these viruses couldn’t be cultured, so these tests made it possible to diagnose cases for which answers would never have been available otherwise.
Finally, technology advances and clinical performance evaluations have continued to hone the accuracy of molecular tests. In addition to R&D efforts that have improved the sensitivity and specificity of molecular diagnostics, comparisons of their results to those of the gold-standard microbiology tests have been better understood. Clinical lab teams have learned that microbiology results are more likely to yield false negative results than was previously thought and that molecular diagnostics offer even better accuracy than initial
Aside from clinical performance, one of the most important aspects of any test in a clinical lab is its reimbursement profile. While some panel tests may be less likely to be reimbursed, molecular diagnostic developers have introduced elements to help labs rein in costs while still optimizing coverage.
One recent development is flexible pricing for panel-based tests, a method that gives labs precise control of testing costs. For some panel tests, labs have found that insurance companies are reluctant to offer reimbursement because they view them as screening tools instead of diagnostic tests. In this situation, some developers allow labs to run an entire molecular panel, but view only results for the candidate pathogens they believe are most likely to be causing the patient’s infection. The other results are masked. If none of the initial results are positive, labs can unmask remaining results until they find an answer, without re-running the test.
The reimbursement innovation here is that labs pay only for the results they view, so if the targeted approach identifies the pathogen causing the disease, as frequently happens, there’s no need to pay for the entire panel. If the patient is immunocompromised or there are other medical factors that indicate a broad panel approach is appropriate, the final cost is still significantly less than it would have been to run individual tests for each of the potential culprits.
Tipping the scales?
New pressures on clinical labs, combined with technological improvements, are increasingly tipping the scales away from microbiology and toward molecular tests. With rapid results, ease of use, and higher accuracy, molecular diagnostics are replacing microbiology options for many types of infectious diseases—and in some cases introducing entirely new tests for pathogens that could never be diagnosed through microbiology.
- Miller SA, Deak E, Humphries R, et al. Comparison of the AmpliVue, BD Max System, and illumigene molecular assays for detection of Group B Streptococcus in antenatal screening specimens. J Clin Microbiol. 2015;53(6):1938–1941.
- Couturier BA, Weight T, Elmer H, Schlaberg R. Antepartum screening for Group B Streptococcus by three FDA-cleared molecular tests and effect of shortened enrichment culture on molecular detection rates. J Clin Microbiol. 2014;52(9):3429-3432.
- Antibiotic resistance: the grim prospect. The Economist. May 21, 2016. www.economist.com/news/briefing/21699115-evolution-pathogens-making-many-medical-problems-worse-time-take-drug-resistance.
- Antimicrobial Resistance: Global Report on Surveillance, 2014. Geneva, Switzerland: World Health Organization, 2014. www.who.int/drugresistance/documents/surveillancereport/en.
- World Health Organization. Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. 2017. www.who.int/medicines/publications/global-priority-list-antibiotic-resistant-bacteria/en.
- Centers for Disease Control and Prevention. Antibiotic/antimicrobial resistance: biggest threats. 2017. www.cdc.gov/drugresistance/biggest_threats.html.
- World Health Organization. Antimicrobial resistance. (fact sheet). 2017. www.who.int/mediacentre/factsheets/fs194/en.
- Ventola CL. The antibiotic resistance crisis: Part 1: causes and threats. P T. 2015;40(4):277–283.
- Hersh AL, Newland JG, Beekmann SE, Polgreen PM, Gilbert DN. Unmet medical need in infectious diseases. Clin Infect Dis. 2012;54(11):1677-1678.
Sherry Dunbar, PhD, MBA, serves as Senior Director of Global Scientific Affairs for Luminex.